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Data released on August 01, 2017

Supporting data for "The draft genome assembly of Rhododendron delavayi Franch. var. delavayi"

Zhang, L; Cai, Y; Xu, P; Ma, L; Li, S; Li, S; Xie, W; Song, J; Peng, L; Yan, H; Zou, L; Ma, Y; Zhang, C; Gao, Q; Wang, J (2017): Supporting data for "The draft genome assembly of Rhododendron delavayi Franch. var. delavayi" GigaScience Database. http://dx.doi.org/10.5524/100331 RIS BibTeX Text

Rhododendron delavayi Franch is globally famous as an ornamental. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at molecular level, which hinders understanding of the nature of its wide adaptability to different environments, evolution, speciation and synthesis of secondary metabolites. Here, we report genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family, and have further applications in genome-assisted cultivar breeding.
The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from nine libraries (with insert sizes ranging from 170bp to 40kb), achieving a raw sequencing depth of 482.61×. After quality filtering, 246.06 Gb of clean reads were obtained, giving 352.55× coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83kb. Gene prediction resulted in the annotation of 32,938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO, and reached 95.97 % and 92.8 % respectively. The Gene annotation completeness was also evaluated by CEGMA and BUSCO, and reached 97.01 % and 87.4 %. Genome annotation revealed that 51.77 % of the R. delavayi genome is composed of transposable elements, and 37.48 % of long terminal repeat elements (LTRs).
The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae, and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties.

Contact Submitter

Additional information:

https://github.com/gigascience/rabbit-genome-assembler

Accessions (data included in GigaDB):

BioProject: PRJNA361437
BioProject: PRJNA358123

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100331.jpg

Funding:

  • Funding body - Yunnan Provincial Science and Technology Department
  • Location - China
  • Award ID - 2016HA005
  • Comment - Science and Technology Talents Training Program
  • Funding body - Yunnan Provincial Science and Technology Department
  • Location - China
  • Award ID - 2014HE002
  • Comment - Innovative Talents Promotion Program
  • Funding body - Yunnan Provincial Science and Technology Department
  • Location - China
  • Award ID - 2016FB058
  • Comment - Applied Basic Research Project of Yunnan Province
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31560225
  • Comment - District science fund project
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31460217
  • Comment - District science fund project

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
leaf321363Rhododendron delavayi Description:DNA extracted from leaf tissue of 50yr...
Analyte type:DNA
Age:50 years
...
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WHYR14030800_B_l1321363Rhododendron delavayi Description:Mixed total RNA extracted from five di...
Analyte type:RNA
Age:50 years
...
+
Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Coding SequenceFASTA19.26 MB2017-07-25
Displaying 41-41 of 41 File(s).

History:

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